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LOC130003713 ATAC-STARR-seq lymphoblastoid silent region 2316 [ Homo sapiens (human) ]

Gene ID: 130003713, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130003713
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2316
Gene type
biological region
Feature type(s)
regulatory: silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence represents an accessible chromatin region that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC130003713 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (43138072..43138131)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (44015569..44015628)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (43633520..43633579)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43492878-43493378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43495973-43496668 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:43507236-43508231 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:43508232-43509226 Neighboring gene microRNA 5100 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:43521643-43522150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43521134-43521642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43522661-43523168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43535603-43536323 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43539799-43540690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43540691-43541582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43544190-43544720 Neighboring gene VISTA enhancer hs2498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43557619-43558120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43558121-43558620 Neighboring gene RET 5' regulatory region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:43572872-43573862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43580156-43580656 Neighboring gene VISTA enhancer hs2326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43596873-43597372 Neighboring gene RET intron 1 enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43600219-43600970 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3282 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:43604510-43604673 Neighboring gene ret proto-oncogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3286 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:43625782-43626382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43626383-43626983 Neighboring gene CSGALNACT2 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2318 Neighboring gene chondroitin sulfate N-acetylgalactosaminyltransferase 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:43655229-43656428 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_12290 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:43686663-43686892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43696895-43697396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2319 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2323 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43700051-43700884 Neighboring gene RasGEF domain family member 1A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43707013-43707615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43711759-43712514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43712515-43713270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43723488-43724298 Neighboring gene uncharacterized LOC107984225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43726130-43726684

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_183159.1 

    Range
    101..160
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    43138072..43138131
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    44015569..44015628
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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